parseDomainInput: Parse domain input file
In BIONF/PhyloProfile: PhyloProfile

parseDomainInput

R Documentation

Parse domain input file

Description

Get all domain annotations for one seed protein IDs.

Usage

parseDomainInput(seed = NULL, inputFile = NULL, type = "file")

Arguments

`seed`	seed protein ID
`inputFile`	name of input file (file name or path to folder contains individual domain files)
`type`	type of data (file" or "folder"). Default = "file".

Value

A dataframe for protein domains including seed ID, its orthologs IDs, sequence lengths, feature names, start and end positions, feature weights (optional) and the status to determine if that feature is important for comparison the architecture between 2 proteins* (e.g. seed protein vs ortholog) (optional).

Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

Examples

seed <- "101621at6656"
inputFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
type <- "file"
parseDomainInput(seed, inputFile, type)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.